Determining a nucleic acid sequence imbalance using multiple markers

1. A method for determining whether a nucleic acid sequence imbalance exists within a biological sample of a female subject pregnant with a fetus having a fetal genome, wherein the biological sample includes a mixture of cell-free nucleic acid molecules from the female subject and from the fetus, the method comprising:

separating the cell-free nucleic acid molecules of the biological sample into a plurality of reactions;

measuring signals from the plurality of reactions;

receiving, at a computer system, quantitative data including the measured signals from the plurality of reactions involving the cell-free nucleic acid molecules from the biological sample, wherein the data includes:

for a plurality of clinically relevant nucleic acid sequences:

(1) first quantitative data indicating a first total amount of the plurality of clinically relevant nucleic acid sequences in the plurality of reactions; and

for a plurality of background nucleic acid sequences:

(2) second quantitative data indicating a second total amount of the plurality of background nucleic acid sequences in the plurality of reactions, wherein the plurality of background nucleic acid sequences are different from any one of the clinically relevant nucleic acid sequences;

determining, by the computer system, the first total amount of the plurality of clinically relevant nucleic acid sequences from the first quantitative data;

determining, by the computer system, the second total amount of the plurality of background nucleic acid sequences from the second quantitative data;

determining a parameter from the first total amount and the second total amount, wherein the parameter provides a relative amount between the first total amount and the second total amount;

comparing the parameter to one or more cutoff values; and

based on the comparison, determining a classification of whether the nucleic acid sequence imbalance exists in the fetal genome for the plurality of clinically relevant nucleic acid sequences.

2. The method of claim 1 , wherein determining the first total amount from the first quantitative data includes:

for each of the clinically relevant nucleic acid sequences:

analyzing the first quantitative data to determine a respective first amount of the clinically relevant nucleic acid sequence in the plurality of reactions,

wherein determining the second total amount from the second quantitative data includes:

for each of the background nucleic acid sequences:

analyzing the second quantitative data to determine a respective second amount of the background nucleic acid sequence in the plurality of reactions,

calculating the first total amount by summing the respective first amounts; and

calculating the second total amount by summing the respective second amounts.

3. The method of claim 2 , further comprising:

correcting the respective first amounts and the respective second amounts before calculating the first total amount and the second total amount.

4. The method of claim 1 , wherein the plurality of reactions are sequencing reactions.

5. The method of claim 4 , wherein the sequencing reactions involve ligation.

6. The method of claim 4 , wherein the sequencing reactions involve synthesis.

7. The method of claim 4 , wherein sequence tags are obtained from the sequencing reactions, and wherein determining the first total amount includes:

aligning the sequence tags to a human genome; and

counting a number of sequence tags that align to the plurality of clinically relevant nucleic acid sequences.

8. The method of claim 4 , further comprising:

enriching the biological sample for the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences; and

subsequently, performing a sequencing of nucleic acid molecules in the enriched biological sample.

9. The method of claim 8 , wherein enriching the biological sample for the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences includes:

using a hybridization-based technique.

10. The method of claim 9 , wherein using the hybridization-based technique includes:

using an oligonucleotide array to select the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences via hybridization.

11. The method of claim 8 , wherein enriching the biological sample for the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences includes:

amplifying the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences.

12. The method of claim 11 , wherein a same primer pair is used to amplify one of the clinically relevant nucleic acid sequences and one of the background nucleic acid sequences.

13. The method of claim 4 , wherein the plurality of reactions include at least one hundred thousand sequencing reactions.

14. The method of claim 1 , further comprising:

prior to performing the plurality of reactions, enriching the biological sample for the plurality of clinically relevant nucleic acid sequences and the plurality of background nucleic acid sequences.

15. The method of claim 1 , further comprising:

determining a fractional concentration of fetal DNA in the biological sample; and

using the fractional concentration of fetal DNA to determine the one or more cutoff values.

16. The method of claim 15 , wherein determining the fractional concentration of fetal DNA in the biological sample includes a quantification of a polymorphic difference between the female subject and the fetus.

17. The method of claim 16 , wherein the quantification includes:

identifying a target polymorphic site at which the female subject is homozygous and the fetus is heterozygous; and

comparing an amount of a fetal-specific allele at the target polymorphic site and an amount of a common allele at the target polymorphic site to determine the fractional concentration of fetal DNA, the common allele not being fetal-specific.

18. The method of claim 15 , wherein the fetus is male, and wherein determining the fractional concentration of fetal DNA in the biological sample includes:

determining a Y chromosome DNA concentration.

19. The method of claim 15 , wherein determining the fractional concentration of fetal DNA in the biological sample includes:

comparing an amount of DNA molecules exhibiting a fetal-specific methylation pattern at a first locus to a total amount of DNA molecules at the first locus.

20. The method of claim 19 , wherein fetal-derived DNA molecules are hypermethylated and maternally-derived DNA molecules are hypomethylated at the first locus.

21. The method of claim 1 , wherein each reaction indicates a presence or absence of a clinically relevant nucleic acid sequence of the plurality of clinically relevant nucleic acid sequences and a background nucleic acid sequence of the plurality of background nucleic acid sequences,

wherein the first quantitative data provides a number of the plurality of reactions positive for the plurality of clinically relevant nucleic acid sequences, and

wherein the second quantitative data provides a number of the plurality of reactions positive for the plurality of background nucleic acid sequences.

22. The method of claim 1 , wherein the clinically relevant nucleic acid sequences are of a first chromosome, wherein the background nucleic acid sequences are of one or more reference chromosomes that are different than the first chromosome, and wherein the classification is of whether the nucleic acid sequence imbalance exists in the fetal genome for the first chromosome.

23. The method of claim 1 , wherein the parameter includes a ratio between the first total amount and the second total amount.

24. The method of claim 1 , wherein the biological sample is plasma.

25. The method of claim 1 , wherein the plurality of clinically relevant nucleic acid sequences are non-consecutive and non-polymorphic.

26. The method of claim 25 , wherein the plurality of background nucleic acid sequences are non-polymorphic.